Ecosystem Monitoring Program
BPA Project Number:  2003-007-00
CR- 309236
Performance/Budget Period: October 1, 2017 – September 30, 2018

Technical Contact/Project Lead:  Catherine Corbett
Lower Columbia Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 240
Fax:  (503) 226-1580
ccorbett@estuarypartnership.org

Contracting Contact: Tom Argent
Lower Columbia River Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 242
Fax:  (503) 226-1580
targent@estuarypartnership.org

BPA Project Manager:  Siena Lopez-Johnston
KEWL-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-3859
amcreason@bpa.gov

SUMMARY

This contract funds two monitoring programs for the lower Columbia River – the Ecosystem Monitoring and Action Effectiveness Monitoring Programs. Both programs are essential for answering key uncertainties about how the lower river functions and understanding ecosystem conditions, how they are changing, and how management actions (e.g., habitat restoration) are improving conditions in the lower river.

Ecosystem Monitoring Program
The Lower Columbia Estuary Partnership (Estuary Partnership) Ecosystem Monitoring Program (EMP) is an integrated status and trends program for the lower Columbia River. The study area extends from the mouth of the estuary to the Bonneville Dam. The program is designed to provide an inventory of the different types of habitats within the lower river; track trends in the overall condition of these habitats and the ecosystem; provide a suite of reference sites for use as end points in the region’s habitat restoration actions, and place findings from management actions into context with the larger ecosystem. The Program is a collaborative effort with NOAA National Marine Fisheries Service (NOAA Fisheries), University of Washington (UW), Oregon Health & Science University (OHSU) and Institute of Applied Ecology, Estuary Technical Group (IAE).

The program was created in 2004 to address the previous lack of research and monitoring within the tidal freshwater section of the lower river (Reaches C-H), resulting in little basic understanding of habitats, fish use, and food web dynamics in this region. At first, the Estuary Partnership and its monitoring partners focused on gaining an understanding of the spatial variability of habitats and fish use (or “status”) across the lower river. From 2004-2012, three to four “status” sites were sampled. We used the eight Hydrogeomorphic Reaches (A-H), identified in the Ecosystem Classification developed through this project in its early years, as the basis for stratifying our sampling. We rotated the “status” sites around the lower river to an unsampled reach each year. In 2007 we initiated a “trend” (or fixed) site to begin understanding the inter-annual variability of conditions. In 2009 we began switching the focus of our sampling to the temporal variability of habitats, fish use and food web dynamics by adding a growing number of “trend” sites and reducing the number of “status” sites. By 2013, there were only the 6 trend sites. The focus of the EMP is on minimally disturbed tidally influenced emergent wetland sites within offchannel sloughs.

The 6 EMP trend sites are 1) Campbell Slough in the Ridgefield National Wildlife Refuge (2005–2017), 2) Whites Island (2009-2017), 3) Franz Lake (2008-2009, 2011-2017), 4) Ilwaco Slough (2010-2017), 5) Welch Island (2010-2014) and 6) Secret River (2010-2013). Habitat structure and hydrology data collection began in 2005, fish data collection began in 2007, fish prey data collection began in 2007, and mainstem water quality data and food web data collection began in 2010.  Data collection includes:
• Salmonid occurrence, composition, growth, diet, condition and residency
• Habitat structure, including physical, biological and chemical properties of habitats
• Food web characteristics, including rates and composition of primary and secondary productivity, abiotic conditions controlling productivity at floodplain habitats and in the mainstem lower river, and role in juvenile salmon diets
• Biogeochemistry of tidal freshwater region of the lower river for comparison to EMP sites and the biogeochemistry of the estuary, key for assessing hypoxia, ocean acidification and climate change impacts.
Because of safety concerns with site conditions for fish sampling, we dropped fish sampling at the Secret River site in 2014 and began testing key uncertainties in lieu of this: 1) how far do upper Columbia River juvenile salmon go up tidal tributaries and 2) does timing of fish sampling within a tidal cycle influence catch. In 2015, we sampled for fish community within tidal reaches of two tributaries (lower Lewis and Grays Rivers). In 2016 and 2017 we tested the timing of sampling during tidal cycles a three EMP sites. In 2018, we will do a seasonal synoptic sampling of fish at some of the AEM sites (see AEM section below).

Applications of Results to Management – funded under BPA’s Columbia River Estuary Ecosystem Restoration Program (CEERP), a primary goal of the EMP is to collect key information on ecological conditions for a range of habitats in the lower river characteristic of those used by out migrating juvenile salmon and provide information towards implementation of the FCRPS BiOp. Information collected describes synoptic conditions and changes over time in vegetated floodplain habitats and the opportunity, capacity and realized function (Simenstad and Cordell 2000) they afford juvenile salmonids. These habitats are the targets of regional restoration efforts, which make the program integral for understanding the success of the regional habitat restoration program. The results of the EMP provide information on ambient environmental conditions and insight into the cumulative effects of existing and new management actions and anthropogenic impacts as they occur.

The EMP has provided key information on a suite of reference sites across the lower river. These sites are used as end points for restoration projects and used in combination with the Action Effectiveness Monitoring and Research (AEMR) Program data described below. Data collected through the EMP on vegetation, elevation, and hydrologic patterns from these sites have been used to create regionally specific restoration design considerations for use by restoration practitioners in designing more successful restoration actions. Patterns include 5 vegetation zones and identified the marsh elevation tolerance of the invasive species, reed canarygrass. Data collected through the EMP have also documented differences in the use of the lower river by different salmonid ESUs.  Data are used for completing templates/applications for project evaluation by the Expert Regional Technical Group and Estuary Partnership Project Review Committee. They are used to inform ecological function models to inform and improve restoration design and within the AEM Program to provide a comparison of conditions within the larger ecosystem to conditions we find at restoration sites.  

Importance of this Program and its Future
• Status and trends monitoring of estuary ecosystem condition–important to “keep pulse on the river” – without this program we can only understand conditions at individual restoration sites and cannot roll-up AEM data and assess benefits of restoration actions without an understanding of what’s also going on across the estuary
• Provides basic information on how estuary functions – despite our growing body of understanding gathered through this and USACE-funded research, there is a continued paucity of research and monitoring in the lower river that limits our basic understanding
• Provides the only inventory of relatively unimpacted habitats across the estuary-river continuum – there are still gaps in the range of habitats such as degraded habitats or within the tidal tributaries
• Provides the only “long-term” dataset of fish use across tidal freshwater sections – ranging 2-10 years; previous studies were temporally or spatially limited
• Provides only information on inter-annual variability of habitat, instream conditions, food web resources and fish use
• Leverages other key programs for more comprehensive analyses:
1. Only consistent toxic contaminant data collection in lower Columbia. Analysis of juvenile Chinook salmon, Chinook stomach contents and macroinvertebrates at sampling sites are completed by NOAA researchers under this program. If the program changes sufficiently, NOAA will no longer be able to leverage the program or have samples to perform and report out analyses. These provide the only consistent information we have in the lower river on concentrations in juvenile salmon and how salmon are being exposed to contaminants.
2. Only systemic mainstem water quality monitoring station above Beaver Army Terminal Center.  OHSU’s Coastal Margin Observation and Prediction (CMOP) station was installed and is now maintained through this program. Our collaboration provides not only the data but our ability to tie into research by OHSU and the Northwest Association of Networked Ocean Observing Systems (NANOOS). The CMOP station is important for modeling and predicting mainstem conditions for the Columbia River Treaty. It is the only monitoring above Beaver Army Terminal and below Bonneville that tracks mainstem biogeochemical water quality conditions.
• Results are used for identifying, designing and monitoring restoration projects – for example:
• Findings on the elevation and inundation period where reed canarygrass thrives (invasive, nuisance species) are used in designing restoration projects by CREST, CLT, WDFW, Estuary Partnership, others to reduce its occurrence at restoration sites
• Results from a focused study on the effects of invasive species (i.e., reed canarygrass) on macroinvertebrate community structure and macrodetrital production indicate the importance of preserving native wetland plant communities.  
• Fish use data are used for ERTG templates by CREST, CLT, WDFW, Estuary Partnership, others and scoring of SBUs by ERTG
• Hydrologic characteristics of estuary regions are used to provide context for inundation anticipated at restoration sites by CLT, WDFW, Estuary Partnership, others
• Sites are used as reference sites for restoration projects by CREST, CLT, WDFW, Estuary Partnership, others. We have done comparisons of reference site conditions with restoration sites action effectiveness data (completed in 2012)
• In stream mainstem conditions used in determining if “greening of river” (macrodetritus versus plankton base of salmon foodweb) is correct and whether system is nutrient limited or nutrient enriched

Past Results - From fiscal years 2004 through 2014, with funding from NPCC/BPA, EMP partners have accomplished the following major tasks: 1) developed a statistically valid, ecosystem-based monitoring plan for the estuary (focusing on juvenile salmon habitats); 2) developed and published a hierarchical estuarine ecosystem classification system (CREEC) in which to base sampling designs and habitat restoration strategies; 3) mapped over 19,000 acres of high and medium priority shallow water bathymetry gaps; 4) mapped land cover of the lower river floodplain in 2000 and 2010; 5) collected water chemistry data and juvenile salmonids to support the creation of three models related to salmonid uptake, transport, and ecological risk of toxic contaminants; 6) collected habitat structure data at 28 sites and comprehensively monitored 22 sites throughout the lower river for habitat structure; salmon occurrence, diet, condition, stock, and growth; prey availability and preference, providing in some areas the only contemporary juvenile salmon use data available; 7) characterized the salmon food web at six “trend” sites representing the estuarine-tidal freshwater gradient; 8) collected abiotic environmental/water column condition data at trend sites annually; 9) installed and maintained a CMOP Land Ocean Biogeochemical Observatory (LOBO) platform above the Willamette River confluence with the Columbia to better understand influence of Willamette biogeochemistry on mainstem conditions; 10) provided technical assistance to the USACE in creation of a terrain model of the lower river, resulting in a seamless bathymetry/topography map which will be invaluable in mapping salmon habitat opportunity in combination with river flow data; 11) provided results for a comparison of macroinvertebrate prey availability, plant biomass, and detrital production at sites dominated by the invasive reed canarygrass versus sites dominated by native vegetation; 12) produced two syntheses of EMP data – one focusing on reporting trends in habitat structure; fish composition, condition, growth rate and prey consumption, and the second focusing on the juvenile salmon food web dynamics and inter-annual variability of the metrics collected under this program.  

In addition, NPCC/BPA funding  is leveraged to allow the Estuary Partnership to accomplish many RME-related coordination activities: 1) convening technical workshops for researchers and managers on topics of interest such as land cover, bathymetry, toxic contaminants, and restoration; 2) providing RME coordination for entities working in the lower river, namely NMFS, PNNL, CREST, USACE, BPA, LCRFB, ODFW, OHSU and others; 3) supported other regional monitoring coordination efforts, including Pacific Northwest Aquatic Monitoring Partnership; 4) acted as a central clearinghouse for GIS and monitoring data while developing mapping website to house data collected in estuary; 5) supported on-going regional toxic contaminants reduction efforts, such as preparing the State of the River Report, presenting monitoring information at the workshops, developing a basin-wide contaminant monitoring strategy with EPA's Toxics Reduction Workgroup; 6) presented monitoring efforts at several regional and national conferences, including the Coastal and Estuarine Research Federation, American Fisheries Society, and Columbia River Estuary Conferences; and 7) participate in regional forums, such as Pacific Estuarine Research Federation (PERS), NANOOS, American Fisheries Society, and Pacific Joint Venture, to share information and coordinate RME and restoration efforts. Information exchanged and gained and networking with other researchers doing related work during these events provides invaluable insight and guidance for future RME and restoration efforts in the lower river.

Current EMP Work -
In 2018 IAE will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at the five trend sites. NOAA Fisheries will monitor salmon and salmon prey, and collect foodweb resources at these sites to provide information on juvenile salmon use of the vegetated and shallow water habitats of the lower Columbia River. NOAA Fisheries will process salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. OHSU will collect food web data at the same sites to characterize conditions supporting juvenile salmonids, specifically rate and composition of primary and secondary productivity, abiotic conditions that limit productivity, and stable isotope analysis of salmon tissue and mucous. OHSU will send benthic cores to UW for processing and taxonomic identification. NOAA will send samples from macroinvertebrate tows and juvenile salmon stomach contents to UW for processing and taxonomic identification. NOAA will continue to operate and maintain a PIT tag array at Campbell Slough to assess salmon residency in floodplain habitats. Additionally, OHSU will continue to maintain the CMOP LOBO Platform in the tidal freshwater section of the lower river for another year. Through this project, CMOP researchers will track and report on 1) seasonal primary production biomass and taxonomy for lower river from Bonneville to plume; 2) sources of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river; and 3) water temperatures, pH, dissolved oxygen levels in tidal freshwater and estuarine (except pH) sections of lower river. The Estuary Partnership Science Work Group will review the data on a periodic basis and recommend possible research studies to address key questions as they arise. All data are analyzed annually and reported to BPA.

Action Effectiveness Monitoring Program
The Action Effectiveness Monitoring program (AEM) was transferred from the Habitat Restoration Program contract (2003-11-00) to this contract in 2013. Since summer 2008 the Estuary Partnership and partners have implemented action effectiveness monitoring based on recommendations from the plan for “Research, Monitoring, and Evaluation for the Federal Columbia River Estuary Program” (Johnson et. al 2008). The Estuary Partnership, with input from the Estuary and Oceanic Subgroup (EOS) and Science Work Group, identified four pilot sites (Mirror Lake, Sandy River Delta, Scappoose Bottomlands, and Fort Clatsop). Sites were chosen to represent different restoration activities (culvert enhancement to improve fish passage; large wood installation; re-vegetation and cattle exclusion; and culvert removal for tidal reconnection), different habitats (bottomland forest, riparian forest, emergent wetland, and brackish wetland), and different geographic reaches of the river (reaches H, G, F, and A, ranging from tidal freshwater in reach H, the Columbia River Gorge, to saltwater intrusion in reach A, Astoria area). Action effectiveness monitoring partners began implementing the Roegner et al. (2009) protocols, which were designed for estuary-wide action effectiveness research, and collected data on parameters such as water quality, sediment accretion, channel cross-sections, vegetation cover, vegetation planting success, salmon, and salmon prey. Action effectiveness monitoring occurred at these sites from 2007-2013, except for the Scappoose Bottomlands site, which was not repeated in 2013 as a result of access issues with the private landowner. Also, NOAA Fisheries installed a pit tag array at the Horsetail Creek restoration site for baseline data collection in 2013; construction at this site occurred in summer 2013. The pit tag array will continue collecting post construction AEM data through 2016.

Applications of Results to Management –
The AEM Program provides information about the efficacy of restoration actions in the tidally influenced areas of the lower Columbia River and estuary.  AEM data shows a quantifiable change in ecosystem condition related to specific restoration actions and helps determine if restoration actions are meeting project sponsors objectives and goals.  The standardization of monitoring metrics allows the ecological impact of restoration actions to be compared across the landscape to help determine the cumulative effects of restoration efforts.  

Past Results-
AEM conducted at pilot sites from 2007-2013 demonstrated the need for standardized monitoring metrics; a site prioritization strategy; an increase in the number of sites monitored; improved data management, analysis and reporting; and a standardized timeline for pre- and post-restoration construction monitoring.  The development of “Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuary” (Roegner et al. 2009) in 2007 and revised in 2009 provided a framework for the when, where, why, and how of action effectiveness monitoring.  In addition, the Estuary Partnership added the Roegner et al. protocols to www.monitoringmethods.org to promote access and sharing.  In 2009, researchers from PNNL, Estuary Partnership, NOAA, USACE and CREST, compiled AEM data from multiple restoration sites in a pilot meta-analysis for the USACE Cumulative Effects of Restoration project.  Also, the standardization of AEM methods allowed data collected at restoration and EMP sites to be compared (e.g., Borde et al. 2012).  Based on lessons learned, the Estuary Partnership with BPA, USACE, and PNNL developed “A Programmatic Plan for Restoration Action Effectiveness Monitoring and Research (AEMR) in the Lower Columbia River and Estuary” (Johnson et al. 2013) to improve and standardize sampling metrics and timelines; create different levels of monitoring efforts (Standard [Level 3], Core [Level 2], and Intensive [Level 1]); designate how these levels will be determined by site; and identify protocols for data management.  
  
In 2013 the Estuary Partnership began implementing the new programmatic AEMR plan. The Estuary Partnership, BPA and US Army Corps of Engineers (USACE), used the programmatic AEMR prioritization process in Johnson et al. (2013) to identify four sites (Kandoll Farm Phase 2 [pre construction], Steamboat Slough [pre construction], Sauvie Island North Unit [pre construction], and Dibblee Point [post construction]) for Level 2 monitoring in 2013. In 2014, we collected Level 2 AEMR data at 5 sites (Kandoll Farm Phase 2 [post construction]; Sauvie Island North Unit Phases 1 and 2 [post and pre construction respectively]; Wallacut Slough [pre construction]; Sandy River Delta [post construction]). In 2015, we collected Level 2 AEMR data at 4 sites (Wallooskee-Youngs [pre], La Center Bottoms [pre], Steamboat Slough [post], Sauvie Island North Unit 2 [post]). In 2016 and 2017, we collected only post construction data at Kandoll Farm Ph 2, Sauvie Island North Unit Ph 1 and 2 respectively, Sandy River Delta and La Center Bottoms, Steamboat Slough, Dibblee Point and Wallacut Slough. Along with these restoration sites, nearby reference sites were identified and monitored to create a pair of sites to ensure the requirements for a Before After Control Impact (BACI) statistical design were met. This results in a total of 8-10 sites per year. AEMR monitoring at restoration and reference sites included characterizing vegetation, sampling macroinvertebrate communities, and collecting channel cross sections and was preformed prior to restoration actions to capture pre-restoration ecological conditions. AEMR project partners CREST and SWCA conducted monitoring using the Roegner et al. (2009) protocols, which are designed for estuary wide action effectiveness monitoring and research. Standardized data collection also ensures data collected for the AEMR program is compatible with data collected under the Ecosystem Monitoring Program.

In addition to Level 2 monitoring, the Estuary Partnership coordinates project sponsors collecting Level 3 AEMR to ensure standardized protocols in sampling design and metrics are being used (water elevation, water temperature, sediment accretion, and photo points) at all restoration sites receiving BPA funding. This coordination role included hosting a 2-day workshop with project sponsors in 2014, working with them to develop site sampling plans for each site and hosting annual meetings to present results from previous year’s AEMR.

Current AEM work-The Estuary Partnership continues to build upon previous AEMR efforts by continuing the collection of Level 2 AEMR data at four to six sites, which are identified by the AEMR Steering Committee (Estuary Partnership, BPA and USACE). The Estuary Partnership will conduct synoptic fish collection at a subset of AEMR sites to establish the presence/absence of salmonid species and determine what stocks of fish are using the restored sites. The Estuary Partnership will also continue coordinating Level 3 data collection efforts of restoration project sponsors, including undertaking field quality assurance audits. The Estuary Partnership compiles and quality checks all Level 3 data, and ensures they are in the correct format for uploading to the USACE Oncor database, when the database becomes available. The Estuary Partnership analyzes all Level 2 data and provides results to BPA in an annual report. A subset of the Level 3 data is included within this report as well.

Coordination Activities - In addition to on the ground work relevant to the EMP and AEM and coordinating activities of lower Columbia partners, we will coordinate with the researchers for the USACE Anadromous Fish Enhancement Program (AFEP), Northwest Power and Conservation Council Ocean subgroup, Pacific Northwest Aquatic Monitoring Program (PNAMP), and the states’ recovery programs to ensure coordination, build monitoring efficiencies, and to increase the consistency of monitoring and sampling protocols used in the LCRE. We will also participate in the AFEP work to build a central RME database for the LCRE so that our data is accessible and usable to interested parties.

2017-2018 OBJECTIVES FOR THE ECOSYSTEM MONITORING and ACTION EFFECTIVENESS MONITORING PROGRAMS INCLUDE:
1. Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at “trend” sites within tidally influenced wetlands of the lower Columbia River.
2. Continue maintenance and data collection at the CMOP LOBO Platform in the tidal freshwater section of the lower Columbia River as well as annual reporting of food web conditions within the entire mainstem lower Columbia River.
3. Collect pre- and post- construction Level 2 AEMR data at priority restoration sites, identified in fall 2017 by the AEMR Steering Committee, and, as funding allows, expand collection (pre-construction) to new priority restoration sites.
4. Coordinate Level 3 AEMR data collection and management with project sponsors (CREST, CLT, Cowlitz Indian Tribe, WDFW), including field quality assurance audits.
5. Develop Annual Reports detailing methods, results, and recommendations.
6. Continue to identify methods of collaborating sampling, data analyses and reporting with USACE-funded RME researchers.